summary

Summary statistics Dicty

## # A tibble: 15 x 3
## # Groups:   bait [12]
##    bait    condition  Unique_bait
##    <fct>   <fct>            <int>
##  1 Gbeta1  Normal               1
##  2 Gbeta2  Normal               1
##  3 Galpha2 starv                1
##  4 Galpha2 veg                  1
##  5 Galpha4 Normal               1
##  6 Galpha8 GDP                  1
##  7 Galpha8 GppNHp               1
##  8 Galpha8 Normal               1
##  9 RasB    Normal               1
## 10 RasC    Normal               1
## 11 RasG1   Normal               1
## 12 RapA    Normal               1
## 13 Rac1    Normal               1
## 14 Ric8    Normal               1
## 15 Roco4   BACKGROUND           1

Show the unique baits count

## # A tibble: 1 x 1
##   Unique_bait_condition
##                   <int>
## 1                    15

Show how many instances (lines) of bait there are

## 
##  Gbeta1  Gbeta2 Galpha2 Galpha4 Galpha8    RasB    RasC   RasG1    RapA    Rac1 
##     876     876    3206    1603    4100     808     998     337     461    1448 
##    Ric8   Roco4 
##    1448    1448

Show how many instances (lines) of condition there are

## 
## BACKGROUND        GDP     GppNHp     Normal      starv        veg 
##       1448       1436       1436      10083       1603       1603

Show total spectral count per bait + condition

## # A tibble: 15 x 3
##    bait    condition  spectral_count
##    <fct>   <fct>               <dbl>
##  1 Gbeta1  Normal              16390
##  2 Gbeta2  Normal              20644
##  3 Galpha2 starv               20155
##  4 Galpha2 veg                 30986
##  5 Galpha4 Normal              27070
##  6 Galpha8 GDP                 13099
##  7 Galpha8 GppNHp              23136
##  8 Galpha8 Normal              23324
##  9 RasB    Normal              12182
## 10 RasC    Normal              22778
## 11 RasG1   Normal              12369
## 12 RapA    Normal               5238
## 13 Rac1    Normal              22196
## 14 Ric8    Normal              18323
## 15 Roco4   BACKGROUND          19376

Show normalized spectral count per bait + condition

## # A tibble: 15 x 3
##    bait    condition  z_score_spectral
##    <fct>   <fct>                 <dbl>
##  1 Gbeta1  Normal             1.72e-14
##  2 Gbeta2  Normal             7.63e-15
##  3 Galpha2 starv              9.37e-16
##  4 Galpha2 veg                1.30e-14
##  5 Galpha4 Normal             7.91e-16
##  6 Galpha8 GDP               -2.50e-14
##  7 Galpha8 GppNHp             4.31e-14
##  8 Galpha8 Normal             1.87e-14
##  9 RasB    Normal             1.05e-14
## 10 RasC    Normal            -2.95e-15
## 11 RasG1   Normal            -4.02e-15
## 12 RapA    Normal            -1.07e-14
## 13 Rac1    Normal             7.24e-15
## 14 Ric8    Normal            -4.04e-15
## 15 Roco4   BACKGROUND         1.28e-15

Show how many uniq uniprot id’s are in the set (dicty has 6 chromosomes and 12500 proteins)

## [1] 2988

uniq proteins per bait_condition

## # A tibble: 15 x 3
## # Groups:   bait [12]
##    bait    condition  `n_distinct(uniprot)`
##    <fct>   <fct>                      <int>
##  1 Gbeta1  Normal                       876
##  2 Gbeta2  Normal                       876
##  3 Galpha2 starv                       1603
##  4 Galpha2 veg                         1603
##  5 Galpha4 Normal                      1603
##  6 Galpha8 GDP                         1436
##  7 Galpha8 GppNHp                      1436
##  8 Galpha8 Normal                      1228
##  9 RasB    Normal                       808
## 10 RasC    Normal                       998
## 11 RasG1   Normal                       337
## 12 RapA    Normal                       461
## 13 Rac1    Normal                      1448
## 14 Ric8    Normal                      1448
## 15 Roco4   BACKGROUND                  1448

Unique proteins per condition

## # A tibble: 6 x 2
##   condition  `n_distinct(uniprot)`
##   <fct>                      <int>
## 1 BACKGROUND                  1448
## 2 GDP                         1436
## 3 GppNHp                      1436
## 4 Normal                      2933
## 5 starv                       1603
## 6 veg                         1603

Unique proteins per bait

## # A tibble: 12 x 2
##    bait    `n_distinct(uniprot)`
##    <fct>                   <int>
##  1 Gbeta1                    876
##  2 Gbeta2                    876
##  3 Galpha2                  1603
##  4 Galpha4                  1603
##  5 Galpha8                  1446
##  6 RasB                      808
##  7 RasC                      998
##  8 RasG1                     337
##  9 RapA                      461
## 10 Rac1                     1448
## 11 Ric8                     1448
## 12 Roco4                    1448

absolute spectral count

Barplot showing the total spectral count for each bait

Barplot showing the absolute spectral count for each condition

Combined spectral count for bait + condition, sum spectral count per group

average spectra

Barplot showing the average spectral count per protein for each bait divided the summed group count by the number of observations in that group so avg count per group

Barplot showing the average spectral count for each condition: divided the summed group count by the number of observations in that group,

Combined spectral count for bait + condition, average spectral count per group

Combined spectral count for bait + condition, average spectral count per group Add overlay with unique proteins

boxplot bait absolute count

Boxplot absolute count vs bait

boxplot condition absolute count

Boxplot count vs condition

boxplot experiment absolute count

Boxplot combined spectral count for bait + condition

z-score normalized boxplot count vs bait

z-score normalized boxplot count vs condition

boxplot count vs condition

z-score normalized boxplot boxplot count vs experiment

Venn diagrams

Venn diagrams over bait

Venn diagrams over condition

overlap proteins per bait_condition

Method to retrieve the overlapping proteins per experiment

Presence/absence protein

Heatmap for uniprot presence/absence over bait, condition or experiment. Filtered on protein

Overlapping proteins

##                  Galpha2_starv Galpha2_veg Galpha4_Normal Galpha8_GDP
## Galpha2_starv             1603        1603           1603        1059
## Galpha2_veg               1603        1603           1603        1059
## Galpha4_Normal            1603        1603           1603        1059
## Galpha8_GDP               1059        1059           1059        1436
## Galpha8_GppNHp            1059        1059           1059        1436
## Galpha8_Normal             957         957            957        1218
## Gbeta1_Normal              736         736            736         739
## Gbeta2_Normal              736         736            736         739
## Rac1_Normal               1098        1098           1098        1131
## RapA_Normal                  0           0              0           0
## RasB_Normal                609         609            609         567
## RasC_Normal                759         759            759         649
## RasG1_Normal               279         279            279         247
## Ric8_Normal               1098        1098           1098        1131
## Roco4_BACKGROUND          1098        1098           1098        1131
##                  Galpha8_GppNHp Galpha8_Normal Gbeta1_Normal Gbeta2_Normal
## Galpha2_starv              1059            957           736           736
## Galpha2_veg                1059            957           736           736
## Galpha4_Normal             1059            957           736           736
## Galpha8_GDP                1436           1218           739           739
## Galpha8_GppNHp             1436           1218           739           739
## Galpha8_Normal             1218           1228           692           692
## Gbeta1_Normal               739            692           876           876
## Gbeta2_Normal               739            692           876           876
## Rac1_Normal                1131           1015           749           749
## RapA_Normal                   0              0             0             0
## RasB_Normal                 567            515           443           443
## RasC_Normal                 649            586           526           526
## RasG1_Normal                247            220           217           217
## Ric8_Normal                1131           1015           749           749
## Roco4_BACKGROUND           1131           1015           749           749
##                  Rac1_Normal RapA_Normal RasB_Normal RasC_Normal RasG1_Normal
## Galpha2_starv           1098           0         609         759          279
## Galpha2_veg             1098           0         609         759          279
## Galpha4_Normal          1098           0         609         759          279
## Galpha8_GDP             1131           0         567         649          247
## Galpha8_GppNHp          1131           0         567         649          247
## Galpha8_Normal          1015           0         515         586          220
## Gbeta1_Normal            749           0         443         526          217
## Gbeta2_Normal            749           0         443         526          217
## Rac1_Normal             1448           0         577         679          264
## RapA_Normal                0         461           0           0            0
## RasB_Normal              577           0         808         570          241
## RasC_Normal              679           0         570         998          300
## RasG1_Normal             264           0         241         300          337
## Ric8_Normal             1448           0         577         679          264
## Roco4_BACKGROUND        1448           0         577         679          264
##                  Ric8_Normal Roco4_BACKGROUND
## Galpha2_starv           1098             1098
## Galpha2_veg             1098             1098
## Galpha4_Normal          1098             1098
## Galpha8_GDP             1131             1131
## Galpha8_GppNHp          1131             1131
## Galpha8_Normal          1015             1015
## Gbeta1_Normal            749              749
## Gbeta2_Normal            749              749
## Rac1_Normal             1448             1448
## RapA_Normal                0                0
## RasB_Normal              577              577
## RasC_Normal              679              679
## RasG1_Normal             264              264
## Ric8_Normal             1448             1448
## Roco4_BACKGROUND        1448             1448
## [1] 279

Simple heatmap with clustering on overlapping proteins per experiment

ggplot heatmap overlapping proteins per experiment

Correlations

raw data

bait heatmap on raw spectra correlation

Condition heatmap on raw spectra correlation

Experiment heatmap on raw spectra correlation

Normalized data

Bait heatmap on normalized spectra correlation

Condition heatmap on normalized spectra correlation

Experiment heatmap on normalized spectra correlation

PCA

bait on raw spectral_count

## Importance of components:
##                              PC1       PC2       PC3       PC4       PC5
## Standard deviation     2500.4102 1578.8117 1143.0789 929.48826 767.77013
## Proportion of Variance    0.4999    0.1993    0.1045   0.06908   0.04713
## Cumulative Proportion     0.4999    0.6992    0.8036   0.87271   0.91984
##                              PC6       PC7       PC8       PC9      PC10
## Standard deviation     677.44725 462.20211 411.55101 320.37644 209.71468
## Proportion of Variance   0.03669   0.01708   0.01354   0.00821   0.00352
## Cumulative Proportion    0.95654   0.97362   0.98716   0.99537   0.99888
##                             PC11      PC12
## Standard deviation     118.26325 1.119e-11
## Proportion of Variance   0.00112 0.000e+00
## Cumulative Proportion    1.00000 1.000e+00

Condition on raw spectral_count

## Importance of components:
##                              PC1       PC2       PC3       PC4       PC5
## Standard deviation     7191.7321 2542.4427 722.60547 539.67106 361.21598
## Proportion of Variance    0.8747    0.1093   0.00883   0.00493   0.00221
## Cumulative Proportion     0.8747    0.9840   0.99287   0.99779   1.00000
##                             PC6
## Standard deviation     1.66e-11
## Proportion of Variance 0.00e+00
## Cumulative Proportion  1.00e+00

Experiment (bait + condition) on raw spectral_count

## Importance of components:
##                              PC1       PC2       PC3       PC4       PC5
## Standard deviation     1971.9458 1290.9757 838.30393 756.25286 636.05050
## Proportion of Variance    0.4743    0.2033   0.08572   0.06976   0.04935
## Cumulative Proportion     0.4743    0.6776   0.76331   0.83307   0.88242
##                              PC6       PC7       PC8       PC9      PC10
## Standard deviation     595.58323 440.54269 371.26426 355.02771 265.38000
## Proportion of Variance   0.04327   0.02367   0.01681   0.01537   0.00859
## Cumulative Proportion    0.92569   0.94936   0.96617   0.98154   0.99013
##                             PC11      PC12     PC13    PC14      PC15
## Standard deviation     204.91780 171.32312 93.43430 28.3651 5.069e-12
## Proportion of Variance   0.00512   0.00358  0.00106  0.0001 0.000e+00
## Cumulative Proportion    0.99526   0.99884  0.99990  1.0000 1.000e+00

Igraph network plot

Demo Viz functions